Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms

Ultraconserved elements in the human genome likely harbor important biological functions as they are dosage sensitive and are able to direct tissue-specific expression. Because they are under purifying selection, variants in these elements may have a lower frequency in the population but a higher likelihood of association with complex traits. We tested a set of highly constrained SNPs (hcSNPs) distributed genome-wide among ultraconserved and nearly ultraconserved elements for association with seven traits related to reproductive (age at natural menopause, number of children, age at first child, and age at last child) and overall [longevity, body mass index (BMI), and height] fitness. Using up to 24,047 European-American samples from the National Heart, Lung, and Blood Institute Candidate Gene Association Resource (CARe), we observed an excess of associations with BMI and height. In an independent replication panel the most strongly associated SNPs showed an 8.4-fold enrichment of associations at the nominal level, including three variants in previously identified loci and one in a locus (DENND1A) previously shown to be associated with polycystic ovary syndrome. Finally, using 1430 family trios, we showed that the transmissions from heterozygous parents to offspring of the derived alleles of rare (frequency ≤0.5%) hcSNPs are not biased, particularly after adjusting for the rates of genotype missingness and error in the data. The lack of transmission bias ruled out an immediately and strongly deleterious effect due to the rare derived alleles, consistent with the observation that mice homozygous for the deletion of ultraconserved elements showed no overt phenotype. Our study also illustrated the importance of carefully modeling potential technical confounders when analyzing genotype data of rare variants.     

Identification of candidate genes for dyslexia susceptibility on chromosome 18

Background

Six independent studies have identified linkage to chromosome 18 for developmental dyslexia or general reading ability. Until now, no candidate genes have been identified to explain this linkage. Here, we set out to identify the gene(s) conferring susceptibility by a two stage strategy of linkage and association analysis.

Methodology/Principal Findings

Linkage analysis: 264 UK families and 155 US families each containing at least one child diagnosed with dyslexia were genotyped with a dense set of microsatellite markers on chromosome 18. Association analysis: Using a discovery sample of 187 UK families, nearly 3000 SNPs were genotyped across the chromosome 18 dyslexia susceptibility candidate region. Following association analysis, the top ranking SNPs were then genotyped in the remaining samples. The linkage analysis revealed a broad signal that spans approximately 40 Mb from 18p11.2 to 18q12.2. Following the association analysis and subsequent replication attempts, we observed consistent association with the same SNPs in three genes; melanocortin 5 receptor (MC5R), dymeclin (DYM) and neural precursor cell expressed, developmentally down-regulated 4-like (NEDD4L).

Conclusions

Along with already published biological evidence, MC5R, DYM and NEDD4L make attractive candidates for dyslexia susceptibility genes. However, further replication and functional studies are still required.     

Supreme™ laryngeal mask airway use in general Anesthesia for category 2 and 3 Cesarean delivery: a prospective cohort study

Background

The Supreme? laryngeal mask airway (SLMA) is a single-use LMA with double lumen design that allows separation of the respiratory and the alimentary tract, hence potentially reducing the gastric volume and risk of aspiration. The purpose of this prospective cohort study is to evaluate the the role of the SLMA as an airway technique for women undergoing category 2 and 3 Cesarean delivery under general anesthesia.

Methods

We recruited 584 parturients who underwent category 2 or 3 Cesarean delivery under general anesthesia, in which 193 parturients underwent category 2 and 391 parturients underwent category 3 Cesarean delivery. The primary outcome was insertion success rate at 1st attempt in SLMA insertion. The secondary outcomes included anaesthetic, obstetric outcomes and maternal side effects associated with airway device.

Results

The 1st attempt insertion success rate was 98.3%, while the overall insertion success rate was 100%. The mean (Standard deviation) time to effective ventilation was 15.6 (4.4) seconds. Orogastric tube insertion was successful at the 1st attempt in all parturients. There was no clinical evidence of aspiration or regurgitation. No episodes of hypoxemia, laryngospasm or bronchospasm were observed intra-operatively. The incidence of complications was low and with good maternal satisfaction reported.

Conclusions

The SLMA could be an alternative effective airway in category 2 and 3 parturients emergency Cesarean Delivery under general anesthesia in a carefully-selected obstetric population.

Trial registration

Clinical Trials Registration: Clinicaltrials.gov Registration NCT02026882. Registered on December 31, 2013.

     

Mechanism of Na‐Ion Storage in Hard Carbon Anodes Revealed by Heteroatom Doping

Hard carbon is the leading candidate anode for commercialization of Na‐ion batteries. Hard carbon has a unique local atomic structure, which is composed of nanodomains of layered rumpled sheets that have short‐range local order resembling graphene within each layer, but complete disorder along the c‐axis between layers. A primary challenge holding back the development of Na‐ion batteries is that a complete understanding of the structure–capacity correlations of Na‐ion storage in hard carbon has remained elusive. This article presents two key discoveries: first, the characteristics of hard carbons structure can be modified systematically by heteroatom doping, and second, that these structural changes greatly affect Na‐ion storage properties, which reveals the mechanisms for Na storage in hard carbon. Specifically, via P or S doping, the interlayer spacing is dilated, which extends the low‐voltage plateau capacity, while increasing the defect concentrations with P or B doping leads to higher sloping sodiation capacity. The combined experimental studies and first principles calculations reveal that it is the Na‐ion‐defect binding that corresponds to the sloping capacity, while the Na intercalation between graphenic layers causes the low‐potential plateau capacity. The understanding suggests a new design principle of hard carbon anode: more reversibly binding defects and dilated turbostratic domains, given that the specific surface area is maintained low.     

T Cell receptor clonotype influences epitope hierarchy in the CD8+ T cell response to respiratory syncytial virus infection

CD8+ T cell responses are important for recognizing and resolving viral infections. To better understand the selection and hierarchy of virus-specific T cell responses, we compared the T cell receptor (TCR) clonotype in parent and hybrid strains of respiratory syncytial virus-infected mice. K(d)M2(82-90) (SYIGSINNI) in BALB/c and D(b)M(187-195) (NAITNAKII) in C57Bl/6 are both dominant epitopes in parent strains but assume a distinct hierarchy, with K(d)M2(82-90) dominant to D(b)M(187-195) in hybrid CB6F1/J mice. The dominant K(d)M2(82-90) response is relatively public and is restricted primarily to the highly prevalent Vβ13.2 in BALB/c and hybrid mice, whereas D(b)M(187-195) responses in C57BL/6 mice are relatively private and involve multiple Vβ subtypes, some of which are lost in hybrids. A significant frequency of TCR CDR3 sequences in the D(b)M(187-195) response have a distinct "(D/E)WG" motif formed by a limited number of recombination strategies. Modeling of the dominant epitope suggested a flat, featureless structure, but D(b)M(187-195) showed a distinctive structure formed by Lys(7). The data suggest that common recombination events in prevalent Vβ genes may provide a numerical advantage in the T cell response and that distinct epitope structures may impose more limited options for successful TCR selection. Defining how epitope structure is interpreted to inform T cell function will improve the design of future gene-based vaccines.     

TAPAS-1, a novel microdomain within the unique N-terminal region of the PDE4A1 cAMP-specific phosphodiesterase that allows rapid, Ca2+-triggered membrane association with selectivity for interaction with phosphatidic acid

Here we identify an 11-residue helical module in the unique N-terminal region of the cyclic AMP-specific phosphodiesterase PDE4A1 that determines association with phospholipid bilayers and shows a profound selectivity for interaction with phosphatidic acid (PA). This module contains a core bilayer insertion unit that is formed by two tryptophan residues, Trp(19) and Trp(20), whose orientation is optimized for bilayer insertion by the Leu(16):Val(17) pairing. Ca(2+), at submicromolar levels, interacts with Asp(21) in this module and serves to gate bilayer insertion, which is completed within 10 ms. Selectivity for interaction with PA is suggested to be achieved primarily through the formation of a charge network of the form (Asp(21-):Ca(2+):PA(2-):Lys(24+)) with overall neutrality at the bilayer surface. This novel phospholipid-binding domain, which we call TAPAS-1 (tryptophan anchoring phosphatidic acid selective-binding domain 1), is here identified as being responsible for membrane association of the PDE4A1 cAMP-specific phosphodiesterase. TAPAS-1 may not only serve as a paradigm for other PA-binding domains but also aid in detecting related phospholipid-binding domains and in generating simple chimeras for conferring membrane association and intracellular targeting on defined proteins.     

Variation in growth in Sandwich Tern chicks Sterna sandvicensis and the consequences for pre- and post-fledging mortality

Fitness consequences of variation in body mass growth and body condition were studied in a Sandwich Tern Sterna sandvicensis colony on Griend, Dutch Wadden Sea, during 1990–2000. Body mass increment during the linear growth phase predicted nestling survival probabilities accurately. Chicks growing less than 8 g per day had low survival probabilities until fledging, but within a range of 8–11 g per day growth only small effects on chick survival were observed. Effects of slow growth on survival became obvious after about 10 days after hatching. Slow growing chicks reached a much lower fledging mass, whereas slow growth had only small effects on structural size at fledging. Body condition of the chicks was highly variable and had strong effects on survival until fledging. However, body condition during the nestling stage did not influence post-fledging survival. Body condition at fledging had no effects on post-fledging survival and did not affect final mass or body size. It is argued that low fledging mass can be overcome soon after fledging, as parents take their fledglings closer to the foraging areas, thereby avoiding high rates of kleptoparasitism by Black-headed Gulls Larus ridibundus .     

Planar cell polarity in the inner ear: how do hair cells acquire their oriented structure?

Sensory hair cells in the ear and lateral line have an asymmetrical hair-bundle structure, essential for their function as directional mechanotransducers. We examine four questions: (1) how does the planar asymmetry of the individual hair cell originate? (2) How are the orientations of neighboring hair cells coordinated? (3) How is the orientation of a group of hair cells controlled in relation to the ear as a whole? (4) How does the initial cell asymmetry lead to creation of the asymmetrical hair bundle? Studies of the development of hairs and bristles in Drosophila, combined with genetic data from vertebrates, suggest that the answer to questions (1) and (2) lies in asymmetries that develop at the cell cortex and at cell-cell junctions, generated by products of a set of primary planar cell polarity genes, including the transmembrane receptor Frizzled. A separate and largely independent mechanism controls asymmmetric allocation of cell fate determinants such as Numb at mitosis, in Drosophila and possibly in the ear also. Little is known about long-range signals that might orient hair cells globally in the ear, but progress has been made in identifying a set of genes responsible for read-out of the primary polarity specification. These genes, in flies and vertebrates, provide a link to assembly of the polarized cytoskeleton; myosin VIIA appears to belong in this group. The mechanism creating the staircase pattern of stereocilium lengths is unknown, but could involve regulation of stereocilium growth by Ca(2+) ions entering via transduction channels.     

Simultaneous reconstruction of the secondary bilateral cleft lip and nasal deformity: Abbé flap revisited

The purpose of this retrospective study was to review the method of using the Abbé flap for correction of secondary bilateral cleft lip deformity in selected patients with tight upper lip, short prolabium, lack of acceptable philtral column and Cupid's bow definition, central vermilion deficiency, irregular lip scars, and associated nasal deformity. A total of 39 patients with the bilateral cleft lip nasal deformity received Abbé flap and simultaneous nasal reconstruction during a period of 6 years. Mean patient age at the time of the operation was 19.1 years, and ranged from 6.6 to 38.5 years. The average follow-up period was 1.8 years. Fourteen patients had prior orthognathic operations. The Abbé flap was designed 13 to 14 mm in length and 8 to 9 mm in width and contained full-thickness tissue from the central lower lip, with a slightly narrow reverse-V caudal end. The prolabium, including the scars and central vermilion, was excised. Lengthening procedures of the upper lip segments were performed if vertical deficiency existed. Part of the prolabial skin was preserved and mobilized for columellar elongation, if indicated. Open rhinoplasty was carried out with or without cartilage graft for columella and nasal tip reconstruction. Reduction of the alar width and nostrils was achieved by a Z-plasty or excision of scar tissue at the nostril floor. The Abbé flap was then transposed cephalad, insetting into the median defect and sutured in layers. The results demonstrated no flap problems or perioperative complications. Seven patients needed further minor revisions on the nose and/or lip. Laser treatment was used to improve the lip scars in three patients. The patients were satisfied with the final outcome and found the lower lip scars acceptable. In conclusion, the described technique of Abbé flap and simultaneous rhinoplasty is an effective reconstructive method for select patients with bilateral cleft lip and nasal deformity.